diff --git a/apps/web/src/app/api/mcp/route.test.ts b/apps/web/src/app/api/mcp/route.test.ts
index 68b8b206..ca515ff5 100644
--- a/apps/web/src/app/api/mcp/route.test.ts
+++ b/apps/web/src/app/api/mcp/route.test.ts
@@ -120,7 +120,7 @@ describe('POST /api/mcp', () => {
   })
 
   it('rejects oversized requests before authentication', async () => {
-    const response = await POST(createRequest({ headers: { 'content-length': String(64 * 1024 + 1) } }))
+    const response = await POST(createRequest({ headers: { 'content-length': String(10 * 1024 * 1024 + 1) } }))
 
     expect(response.status).toBe(413)
     await expect(response.json()).resolves.toEqual({ error: 'payload_too_large' })
diff --git a/apps/web/src/app/api/mcp/route.ts b/apps/web/src/app/api/mcp/route.ts
index 8e2da413..6a45feae 100644
--- a/apps/web/src/app/api/mcp/route.ts
+++ b/apps/web/src/app/api/mcp/route.ts
@@ -8,7 +8,7 @@ import { auditService, mcpSettingsService, rateLimitService } from '@/lib/servic
 export const runtime = 'nodejs'
 export const dynamic = 'force-dynamic'
 
-const MCP_MAX_BODY_BYTES = 64 * 1024
+const MCP_MAX_BODY_BYTES = 10 * 1024 * 1024
 const MCP_PREAUTH_RATE_LIMIT_MAX = 300
 const MCP_PREAUTH_RATE_LIMIT_WINDOW_MS = 60 * 1000
 const MCP_TOKEN_RATE_LIMIT_MAX = 100
diff --git a/apps/web/src/components/workspace/__tests__/file-tree-panel.test.tsx b/apps/web/src/components/workspace/__tests__/file-tree-panel.test.tsx
index 7d160b3c..fb473c14 100644
--- a/apps/web/src/components/workspace/__tests__/file-tree-panel.test.tsx
+++ b/apps/web/src/components/workspace/__tests__/file-tree-panel.test.tsx
@@ -53,6 +53,112 @@ describe("FileTreePanel", () => {
     expect(onDownloadFile).toHaveBeenCalledWith("alpha.md");
   });
 
+  it("auto-expands top-level directories when nodes arrive", async () => {
+    render(
+      <FileTreePanel
+        nodes={nodes}
+        activePath={null}
+        onSelect={() => {}}
+      />
+    );
+
+    expect(await screen.findByRole("button", { name: /notes.md/i })).toBeTruthy();
+  });
+
+  it("expands ancestor directories of the active file path", async () => {
+    const deepNodes: WorkspaceFileNode[] = [
+      {
+        id: "docs",
+        name: "docs",
+        path: "docs",
+        type: "directory",
+        children: [
+          {
+            id: "docs/research",
+            name: "research",
+            path: "docs/research",
+            type: "directory",
+            children: [
+              {
+                id: "docs/research/analysis.md",
+                name: "analysis.md",
+                path: "docs/research/analysis.md",
+                type: "file",
+              },
+            ],
+          },
+        ],
+      },
+    ];
+
+    render(
+      <FileTreePanel
+        nodes={deepNodes}
+        activePath="docs/research/analysis.md"
+        onSelect={() => {}}
+      />
+    );
+
+    expect(await screen.findByRole("button", { name: /analysis.md/i })).toBeTruthy();
+  });
+
+  it("preserves user-collapsed directories on subsequent updates", async () => {
+    const onSelect = vi.fn();
+
+    const { rerender } = render(
+      <FileTreePanel
+        nodes={nodes}
+        activePath={null}
+        onSelect={onSelect}
+      />
+    );
+
+    const docsButton = await screen.findByRole("button", { name: /^docs$/i });
+    expect(screen.getByRole("button", { name: /notes.md/i })).toBeTruthy();
+
+    fireEvent.click(docsButton);
+
+    expect(screen.queryByRole("button", { name: /notes.md/i })).toBeNull();
+
+    rerender(
+      <FileTreePanel
+        nodes={nodes}
+        activePath="alpha.md"
+        onSelect={onSelect}
+      />
+    );
+
+    expect(screen.queryByRole("button", { name: /notes.md/i })).toBeNull();
+  });
+
+  it("expands a collapsed dir when navigating to a file inside it", async () => {
+    const onSelect = vi.fn();
+
+    const { rerender } = render(
+      <FileTreePanel
+        nodes={nodes}
+        activePath={null}
+        onSelect={onSelect}
+      />
+    );
+
+    const docsButton = await screen.findByRole("button", { name: /^docs$/i });
+    expect(screen.getByRole("button", { name: /notes.md/i })).toBeTruthy();
+
+    fireEvent.click(docsButton);
+    expect(screen.queryByRole("button", { name: /notes.md/i })).toBeNull();
+
+    rerender(
+      <FileTreePanel
+        nodes={nodes}
+        activePath="docs/notes.md"
+        onSelect={onSelect}
+      />
+    );
+
+    expect(await screen.findByRole("button", { name: /notes.md/i })).toBeTruthy();
+  });
+
   it("supports downloading files from search results too", async () => {
     const onDownloadFile = vi.fn();
 
diff --git a/apps/web/src/components/workspace/__tests__/workspace-shell.test.tsx b/apps/web/src/components/workspace/__tests__/workspace-shell.test.tsx
index f5cbf6bb..35a3b1c5 100644
--- a/apps/web/src/components/workspace/__tests__/workspace-shell.test.tsx
+++ b/apps/web/src/components/workspace/__tests__/workspace-shell.test.tsx
@@ -1088,7 +1088,7 @@ describe("WorkspaceShell", () => {
 
     const params = new URLSearchParams(window.location.search);
     expect(params.get("mode")).toBe("flows");
-    expect(params.get("path")).toBe("docs/plan.md");
+    expect(params.get("path")).toBeNull();
 
     rerender(<WorkspaceShell slug="alice" initialWorkspaceMode="flows" />);
     rerender(<WorkspaceShell slug="alice" initialWorkspaceMode="knowledge" />);
diff --git a/apps/web/src/components/workspace/file-tree.tsx b/apps/web/src/components/workspace/file-tree.tsx
index 5a26c553..b76bf85a 100644
--- a/apps/web/src/components/workspace/file-tree.tsx
+++ b/apps/web/src/components/workspace/file-tree.tsx
@@ -1,6 +1,6 @@
 "use client";
 
-import { useMemo, useState, type MouseEvent } from "react";
+import { useEffect, useRef, useState, type MouseEvent } from "react";
 import { CaretRight, File, Folder, FolderOpen } from "@phosphor-icons/react";
 
 import { cn } from "@/lib/utils";
@@ -18,19 +18,58 @@ type FileTreeProps = {
 
 type TreeState = Record<string, boolean>;
 
+function getAncestorPaths(filePath: string): string[] {
+  const segments = filePath.split("/");
+  const ancestors: string[] = [];
+  for (let i = 1; i < segments.length; i++) {
+    ancestors.push(segments.slice(0, i).join("/"));
+  }
+  return ancestors;
+}
+
 export function FileTree({ nodes, activePath, onSelect, onFileContextMenu }: FileTreeProps) {
-  const initialExpanded = useMemo<TreeState>(() => {
-    const state: TreeState = {};
-    nodes.forEach((node) => {
-      if (node.type === "directory") state[node.path] = true;
-    });
-    return state;
-  }, [nodes]);
+  const [expanded, setExpanded] = useState<TreeState>({});
+  const userCollapsedRef = useRef(new Set<string>());
+  const prevActivePathRef = useRef(activePath);
 
-  const [expanded, setExpanded] = useState<TreeState>(initialExpanded);
+  useEffect(() => {
+    const activePathChanged = activePath !== prevActivePathRef.current;
+    prevActivePathRef.current = activePath;
+
+    setExpanded((prev) => {
+      const next = { ...prev };
+      let changed = false;
+      for (const node of nodes) {
+        if (node.type === "directory" && !(node.path in prev)) {
+          next[node.path] = true;
+          changed = true;
+        }
+      }
+      if (activePath) {
+        for (const ancestor of getAncestorPaths(activePath)) {
+          if (activePathChanged) {
+            userCollapsedRef.current.delete(ancestor);
+          }
+          if (!next[ancestor] && !userCollapsedRef.current.has(ancestor)) {
+            next[ancestor] = true;
+            changed = true;
+          }
+        }
+      }
+      return changed ? next : prev;
+    });
+  }, [nodes, activePath]);
 
   const toggle = (path: string) => {
-    setExpanded((prev) => ({ ...prev, [path]: !prev[path] }));
+    setExpanded((prev) => {
+      const wasOpen = prev[path];
+      if (wasOpen) {
+        userCollapsedRef.current.add(path);
+      } else {
+        userCollapsedRef.current.delete(path);
+      }
+      return { ...prev, [path]: !wasOpen };
+    });
   };
 
   const renderNode = (node: WorkspaceFileNode, depth: number) => {
diff --git a/apps/web/src/components/workspace/workspace-shell.tsx b/apps/web/src/components/workspace/workspace-shell.tsx
index 81dfab5c..97b9a061 100644
--- a/apps/web/src/components/workspace/workspace-shell.tsx
+++ b/apps/web/src/components/workspace/workspace-shell.tsx
@@ -781,12 +781,36 @@ export function WorkspaceShell({
     return normalized;
   }, [initialFilePath]);
 
-  const [openFilePaths, setOpenFilePaths] = useState<string[]>(
-    safeInitialFilePath ? [safeInitialFilePath] : []
-  );
-  const [activeFilePath, setActiveFilePath] = useState<string | null>(
-    safeInitialFilePath
-  );
+  const openFilesStorageKey = `arche.workspace.${slug}.openFiles`;
+
+  const [openFilePaths, setOpenFilePaths] = useState<string[]>(() => {
+    if (typeof window === "undefined") return safeInitialFilePath ? [safeInitialFilePath] : [];
+    try {
+      const stored = window.localStorage.getItem(openFilesStorageKey);
+      if (!stored) return safeInitialFilePath ? [safeInitialFilePath] : [];
+      const parsed = JSON.parse(stored) as { paths?: string[]; active?: string | null };
+      const paths = Array.isArray(parsed.paths) ? parsed.paths.filter((p): p is string => typeof p === "string") : [];
+      if (safeInitialFilePath && !paths.includes(safeInitialFilePath)) {
+        paths.push(safeInitialFilePath);
+      }
+      return paths.length > 0 ? paths : safeInitialFilePath ? [safeInitialFilePath] : [];
+    } catch {
+      return safeInitialFilePath ? [safeInitialFilePath] : [];
+    }
+  });
+
+  const [activeFilePath, setActiveFilePath] = useState<string | null>(() => {
+    if (safeInitialFilePath) return safeInitialFilePath;
+    if (typeof window === "undefined") return null;
+    try {
+      const stored = window.localStorage.getItem(openFilesStorageKey);
+      if (!stored) return null;
+      const parsed = JSON.parse(stored) as { paths?: string[]; active?: string | null };
+      return typeof parsed.active === "string" ? parsed.active : null;
+    } catch {
+      return null;
+    }
+  });
   const [fileCache, setFileCache] = useState<FileContentCache>({});
   const fileCacheRef = useRef(fileCache);
 
@@ -794,6 +818,73 @@ export function WorkspaceShell({
     fileCacheRef.current = fileCache;
   }, [fileCache]);
 
+  useEffect(() => {
+    if (typeof window === "undefined") return;
+    const params = new URLSearchParams(window.location.search);
+    if (isKnowledgeMode && activeFilePath) {
+      params.set("path", activeFilePath);
+    } else {
+      params.delete("path");
+    }
+    const query = params.toString();
+    window.history.replaceState(
+      window.history.state,
+      "",
+      query ? `/w/${slug}?${query}` : `/w/${slug}`
+    );
+  }, [activeFilePath, isKnowledgeMode, slug]);
+
+  useEffect(() => {
+    if (typeof window === "undefined") return;
+    try {
+      if (openFilePaths.length === 0) {
+        window.localStorage.removeItem(openFilesStorageKey);
+      } else {
+        window.localStorage.setItem(
+          openFilesStorageKey,
+          JSON.stringify({ paths: openFilePaths, active: activeFilePath })
+        );
+      }
+    } catch {
+      // ignore storage errors
+    }
+  }, [openFilePaths, activeFilePath, openFilesStorageKey]);
+
+  const initialOpenFilePathsRef = useRef(openFilePaths);
+  useEffect(() => {
+    const pathsToLoad = initialOpenFilePathsRef.current.filter(
+      (p) => !fileCacheRef.current[p]
+    );
+    if (pathsToLoad.length === 0) return;
+    void Promise.all(
+      pathsToLoad.map((filePath) =>
+        readWorkspaceFile(filePath).then((result) => {
+          if (!result) return null;
+          return { filePath, result };
+        })
+      )
+    ).then((results) => {
+      const loaded = results.filter(
+        (r): r is NonNullable<typeof r> => r !== null
+      );
+      if (loaded.length === 0) return;
+      setFileCache((prev) => {
+        const next = { ...prev };
+        for (const { filePath, result } of loaded) {
+          next[filePath] = {
+            content: result.content,
+            type: result.type,
+            title: filePath.split("/").pop() ?? filePath,
+            updatedAt: "Just now",
+            size: `${(result.content.length / 1024).toFixed(1)} KB`,
+            hash: result.hash,
+          };
+        }
+        return next;
+      });
+    });
+  }, [readWorkspaceFile]);
+
   const refreshOpenFilesCache = useCallback(async () => {
     if (openFilePaths.length === 0) return;